In the new teaser for Mass Effect 2, developer Bioware hints that Commander Shepard may have met an untimely end in the events leading up to the sequel:

In a depressing but predictable turn, waves of grim and spastic Mass Effect fans staged a revolt on the Bioware forums.  In response, several Bioware developers calmly reminded everyone to keep their Mass Effect save files.  A million angry voices then cried out “Don’t tell me what to do!  Your people killed Shepard!”, followed by the defiant deletetion of all save files.

If Bioware actually intended to kill off Mass Effect’s main character, they probably wouldn’t spoil it in a teaser, which, by the way, is really short on substance.  Besides faking us out with the Shepard death, it looks like we’ll be fighting the Geth, which means that the Reapers won’t be too far behind.